---
date: 2017-07-24T00:11:02+01:00
title: Documentation
weight: 10
---



<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
<div id="vignettes" class="section level2">
<h2><i class="fa fa-book"></i> Vignettes</h2>
<ul>
<li><a href="https://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html">ChIPseeker: an R package for ChIP peak Annotation, Comparison and Visualization</a></li>
</ul>
</div>
<div id="blog-posts" class="section level2">
<h2><i class="fa fa-wordpress"></i> Blog posts</h2>
<div id="news-and-updates" class="section level3">
<h3><i class="fa fa-angle-double-right"></i> News and updates</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2015/04/bioc-31-news-of-my-bioc-packages">BioC 3.1: NEWS of my BioC packages</a></li>
<li><a href="https://guangchuangyu.github.io/2015/10/bioc-32-news-of-my-bioc-packages">BioC 3.2: NEWS of my BioC packages</a></li>
<li><a href="https://guangchuangyu.github.io/2016/05/bioc-33-news-of-my-bioc-packages/">BioC 3.3: NEWS of my BioC packages</a></li>
<li><a href="https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages">BioC 3.4: NEWS of my BioC packages</a></li>
<li><a href="https://guangchuangyu.github.io/2015/08/parsing-bed-coordinates">parsing BED coordinates</a></li>
<li><a href="https://guangchuangyu.github.io/2015/07/chipseeker-an-r/bioconductor-package-for-chip-peak-annotation-comparison-and-visualization">ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization</a></li>
</ul>
</div>
<div id="annotation" class="section level3">
<h3><i class="fa fa-angle-double-right"></i> Annotation</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2014/04/chipseeker-for-chip-peak-annotation">ChIPseeker for ChIP peak annotation</a></li>
<li><a href="https://guangchuangyu.github.io/2014/10/multiple-annotation-in-chipseeker">multiple annotation in ChIPseeker</a></li>
</ul>
</div>
<div id="visualization" class="section level3">
<h3><i class="fa fa-angle-double-right"></i> Visualization</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2014/04/visualization-methods-in-chipseeker">visualization methods in ChIPseeker</a></li>
<li><a href="https://guangchuangyu.github.io/2015/07/upsetplot-in-chipseeker">upsetplot in ChIPseeker</a></li>
<li><a href="https://guangchuangyu.github.io/2016/02/covplot-supports-grangeslist">covplot supports GRangesList</a></li>
</ul>
</div>
<div id="functional-enrichment-analysis" class="section level3">
<h3><i class="fa fa-angle-double-right"></i> Functional Enrichment Analysis</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2015/08/functional-enrichment-analysis-with-ngs-data">functional enrichment analysis with NGS data</a></li>
</ul>
</div>
<div id="comparison" class="section level3">
<h3><i class="fa fa-angle-double-right"></i> Comparison</h3>
<ul>
<li><a href="https://guangchuangyu.github.io/2015/10/chipseq-data-mining-with-chipseeker">ChIPseq data mining with ChIPseeker</a></li>
</ul>
<p><i class="fa fa-hand-o-right"></i> Find out more on <a href="https://guangchuangyu.github.io/tags/chipseeker/" class="uri">https://guangchuangyu.github.io/tags/chipseeker/</a>.</p>
</div>
</div>
<div id="qa" class="section level2">
<h2><i class="fa fa-support"></i> Q&amp;A</h2>
<ul>
<li><a href="https://www.biostars.org/p/214557/#214623">how to read multiple peak files</a></li>
<li><a href="https://www.biostars.org/p/215069">annotate lncRNA</a></li>
</ul>
</div>
<div id="workflow" class="section level2">
<h2><i class="fa fa-gift"></i> Workflow</h2>
<ul>
<li><a href="http://compbio.ucdenver.edu/Hunter_lab/Phang/resources/Tzu-Software/ChIPseq.Analysis.html">ChIPseq Analysis</a></li>
<li><a href="http://biocluster.ucr.edu/~rkaundal/workshops/R_feb2016/ChIPseq/ChIPseq.html">NGS data analysis with R / Bioconductor: ChIP-Seq workflow</a></li>
<li><a href="http://f1000research.com/articles/5-1542/v1">TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages</a></li>
</ul>
</div>
